Methods of quantifying N2-(1-carboxyethyl)-2′-deoxy-guanosine (CEdG) and synthesis of oligonucleotides containing CEdG

ABSTRACT

Methods of quantifying N 2 -carboxyethyl-2′-deoxyguanosine (CEdG) levels in biological samples and comparing those levels to known normal levels can diagnose a number of disorders, including diabetes and cancer. Methods can also determine whether therapies for disorders are effective by measuring CEdG levels before and after treatment. Measurement of CEdG levels occurs using liquid chromatography electrospray ionization tandem mass spectrometry.

PRIORITY CLAIM

This application is a continuation of U.S. application Ser. No.14/536,299, filed Nov. 7, 2014, issuing as U.S. Pat. No. 9,855,233 onJan. 2, 2018, which is a continuation of U.S. application Ser. No.13/308,433, filed Nov. 30, 2011, which is a divisional of U.S.application Ser. No. 12/538,854, filed Aug. 10, 2009, which claims thebenefit of U.S. Provisional Application Ser. No. 61/087,393, filed Aug.8, 2008, all of which are incorporated herein by reference.

GOVERNMENT INTEREST

The present invention was made with government support under City ofHope's Cancer Center Support Grant (NIH Grant No. P30 CA33572) and theCalifornia Breast Cancer Research Program for a pre-doctoral fellowshipto D. Tamae (14GB-0162). The government has certain rights in thepresent invention.

BACKGROUND

Methylglyoxal (MG) is a highly reactive electrophile and is present atmicromolar levels in many foods and most living organisms. MG is a majorenvironmental breakdown product of carbohydrates. MG is also generatedbiochemically during glycolysis via elimination of phosphate from thecommon enediol intermediate resulting from deprotonation ofdihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Additionalendogenous sources of MG include the catabolism of threonine and theP450 mediated oxidation of ketone bodies and the oxidative breakdown ofDNA and RNA under acidic conditions. MG is a probable mutagen in vivo.

Methylglyoxal induces G>T and G>C transversions, as well as a largenumber (50%) of multibase deletions. Since 89% of the base substitutionmutations are observed at guanosine, andN²-(1-Carboxyethyl)-2′-Deoxy-Guanosine (“CEdG”) is the predominantadduct formed from reaction of MG with DNA, this pattern oftransversions arises from CEdG (as primer extension assays usingoligonucleotide templates containing CEdG have evidenced). The presenceof CEdG in DNA has also been shown to induce single-strand breaks,suggesting an alternative mechanism by which this adduct may contributeto genetic instability.

Glycation results when a sugar, such as fructose or glucose,non-enzymatically links to a protein or lipid. Glycation typicallyimpairs the function of the molecules to which it binds. Methylglyoxalreacts readily with nucleophilic moieties on proteins, lipids and DNA toproduce covalent adducts known as advanced glycation end-products(AGEs). Protein AGEs are well characterized and these highly modifiedproteins have been proposed to play a role in the various pathologiesassociated with diabetes, cancer, aging, and Alzheimers disease. Thefirst clear correlation between abnormal levels of a protein-AGE and ahuman disease (diabetes) was described in 1969 for the hemoglobinHbA_(1c) adduct by Rahbar et al. Since then, hemoglobin HbA_(1c) hasbecome a commonly used biomarker for the diagnosis and treatmentmonitoring of diabetes.¹¹⁻¹³ Accordingly, there is continued interest inthe development of novel, more sensitive assays for the quantitativemeasurement of biomolecule-derived AGEs to complement and extend theclinical biomarker repertoire, as well as to assist in elucidating theirrole in pathology.

Approximately a dozen protein-AGEs have been characterized and LC-MS/MSmethods have been described for their quantitative measurement. Choosingan appropriate protein-AGE biomarker for evaluating the glycation statusof a particular target tissue or organ is complicated by unequalprotein-AGE distributions across different tissues, varying adductstabilities, and the limited availability of stable isotope standardsfor quantification. Glycation adducts of DNA have potential asbiomarkers since all nucleated cells contain the same DNA content andshould reflect the relative level of MG in the target tissue.

In spite of longstanding interest in the role of biopolymer glycation inhuman disease, no generally applicable method for the quantitativedetermination of CEdG has been described. A ³²P post-labeling assay hasbeen used to estimate endogenous levels of CEdG in human buccalepithelial cells of 2-3/10⁷ nucleotides.²⁸ However, although thepost-labeling method offers potential advantages in sensitivity, a majordrawback is that direct analyte verification is not possible. Moreover,post-labeling is prone to artifacts and false positives, and may lead toinaccurate estimation of adduct levels due to several factors includingRNA contamination.

An immunoaffinity-based method for the detection of CEdG using apolyclonal antibody coupled to a diode array HPLC platform has morerecently been described by Schneider et al in 2006. This approach wasused to provide the first demonstration of CEdG in human urine andcultured smooth muscle cells. In some cases, peak identity was confirmedby LC-MS/MS, but quantitation was not practical due to the imprecisenature of immunoaffinity chromatography. A monoclonal-basedimmunohistochemical detection method has also been reported and was usedto demonstrate elevated levels of CEdG in aorta and kidney of diabeticpatients relative to normal controls.³¹ However, antibody-based assaysare primarily of value in qualitative and comparative determinations ofadduct abundance.

To date, there are no reliable quantitative methods for CEdGmeasurement, which is likely due to a lack of suitable isotopicallyenriched standards and other barriers to a reliable quantitative method.Such a method would be a substantial improvement in the art.

SUMMARY

In a first embodiment, advanced glycation end products (AGE), such asN²-carboxyethyl-2′-deoxyguanosine (CEdG), may be quantified in abiological sample using liquid chromatography electrospray ionizationtandem mass spectrometry (LC-ESI-MS/MS) for diagnosis, monitoring, andtreatment of pathologies involving metabolic disorders, includingabnormal glucose metabolism. Such pathologies include diabetes andcancer, amongst other metabolic diseases or disorders. Quantification isachieved by a stable isotope dilution method using an internal standard.When the AGE is CEdG, the internal standard is ¹⁵N₅-CEdG. The advantageof having two stereoisomers of CEdG that can be resolved and quantitatedallows for two independent measurements for the same condition,significantly enhancing the accuracy of the method.

Detecting physiologically elevated or depressed levels of AGE in asample may indicate that the subject from which the sample was taken hasa disease or disorder caused or indicated by such AGE levels. Thequantification method allows for a precise determination of AGE amountsand thus, allows for sensitive determination of AGE levels compared toother samples from the same subject at the same time, other samples fromthe same subject at different time points, or other samples from othersubjects, such as a person known not to be affected by a disease. Forexample, detecting elevated levels of CEdG in a person indicatespredisposition to or the presence of hyperglycemia or diabetes. Reactionof double stranded DNA with MG or glucose in vitro produces primarilyN²-carboxyethyl-2′-deoxyguanosine as a diastereomeric mixture (FIG. 1).The same type of sample may be used to compare between various AGElevels, such as a comparison between AGE levels in a first tissue sampleand a second tissue sample. Alternatively, the AGE levels may becompared between various types of samples so long as the relativephysiological normal level for each type of sample is known.

In another embodiment, internal standards for other AGEs are createdusing the methods disclosed herein for synthesizing the internalstandard of CEdG. Standards for MS are typically identical in structureto the intended analyte, but contain stable isotopes (15N, 13C, 18O) inorder to give a different mass to an otherwise chemically identicalsubstance. The isotope behaves identically to the intended analyte, hasthe same retention on chromatography, and undergoes the same chemistry,and is only distinguishable by mass.

In a different embodiment, the quantification methods described hereinmay also be used to determine the effectiveness of a therapy, which maybe a test compound or other protocol, intended to treat or ameliorate anAGE-related disease or disorder (a “therapeutically effective amount”).Before the therapy is administered, a first biological sample is taken.After the therapy has been administered, a second biological sample istaken. Additional biological samples may also be taken at other timepoints during and/or after the therapy. AGE is quantified in the samplesand the difference between AGE levels in the samples is measured. Otherknown statistical analysis, such as tests for statistical significance,may also be applied. If a successful therapy results in a reduction ofthe level of AGE and such reduction is noted after the administration ofthe therapy, it indicates that the therapy may be working for itsintended purpose. If AGE levels in the sample are static or increasedduring the course of the therapy, it indicates that the therapy may notbe working for its intended purpose of reducing AGE levels. If asuccessful therapy results in an increase of AGE levels with atreatment, the opposite analysis would apply: increases in AGE levelswould indicate the therapy may be working, whereas static or decreasedlevels would indicate that the therapy may not be effective.

Kits for quantifying AGE levels, such as CEdG levels, are alsocontemplated. Such kits facilitate the methods described herein maycontain any of the following: standards such as ¹⁵N₅-CEdG, tubes,labels, reagents such as buffer, and instructions for use.

Another embodiment involves measuring urine samples in an animal modelto monitor the dose dependency of LR-90 as it decreases CEdG levels invivo.

Yet another embodiment is measuring the effect of aromatase inhibitorson CEdG levels, and relatedly, on glycation status. CEdG levels aremeasured in a subject undergoing aromatase inhibitory therapy (AI) todetermine the impact of AI on cognitive function and mental acuity.

A method of measuring CEdG to predict chemosensitivity of tumors and toidentify cancers that may be treated from targeting glyoxalase 1 and/oraldose reductase to restore chemosensitivity is also described. Tumorswith elevated levels of CEdG are more sensitive to chemotherapy. Relatedmethods of inducing production of CEdG or other AGE products in tumorcells or of administering CEdG to tumor cells to induce apoptosis and/orincreased sensitivity to chemotherapy are also provided. Theeffectiveness of radiotherapy may also be tested by measuring CEdG intumors.

A novel synthesis of oligonucleotides containing site-specificallymodified CEdG residues is shown in FIG. 16. Such synthesis facilitatesexperiments using CEdG, such as experiments that investigate thebiological consequences of CEdG substitution in DNA and for serving asinternal standards for assays measuring CEdG.

These and other embodiments are further explained by reference to thedetailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. The two CEdG diastereomers formed from reaction of MG with dG.

FIG. 2. A representative HPLC chromatogram of the reaction of ¹⁵N₅-dGwith dl-glyceraldehyde. Peaks A and B correspond to the twodiastereomers of ¹⁵N₅-CEdG.

FIG. 3. Full scan positive ion ESI-MS spectrum for ¹⁵N₅-CEdGdiastereomer peak A.

FIG. 4. Time course product profiles of the reaction of dG and the A andB stereoisomers of CEdG with 1 M AcOH at 37° C. The inset shows the HPLCchromatogram of the reaction of CEdG-B at 450 min.

FIG. 5. Quantitation of CEdG in normal (light grey) and diabetic (darkgrey) Sprague-Dawley rats. Superscript a (“^(a)”): Ordinate valuesrepresent ad libitum concentrations of the AGE inhibitor drug LR-90(mg/L). *P<0.05 and **P<0.01 vs untreated diabetic animals (Bonferonni'stest)(no asterisks).

FIG. 6. LC-ESI-MS/MS measurements of CEdG diastereomers in calf thymusDNA subjected to various workup procedures. Hydrolyzed samplescorrespond to DNA treated with nuclease P1/alkalinephosphatase/phosphodiesterase. Calf thymus DNA samples were also reactedwith proteinase K (Extracted) prior to hydrolysis. Levels of CEdG weremeasured in the presence or absence of carbonyl scavenger AG.

FIG. 7. Reactions of carbonyl scavengers AG and D-P with MG yieldisomeric aminotriazines (top) and 2-acylthiazolidine (bottom).

FIGS. 8A-C. UV spectra of stock solutions of unlabeled (FIG. 8A) andisotopically labeled CEdG diasteromers (FIGS. 8B-8C). FIG. 8A: UVspectra of CEdG(A)(solid line) and CEdG(B)(dotted line) with no isotopiclabeling. Both samples were diluted 1:50; OD₂₅₅(dG)=12,300 OD/M. ForCEdG(A), XX-49-A, 28.55 mL; diluted OD₂₅₅=0.450; undiluted OD₂₅₅=22.50;conc.=1.83 mM, 52.22 umol @ FW 338.30=17.67 mg. For CEdG(B), XX-49-A,40.61 mL; diluted OD₂₅₅=0.327; undiluted OD₂₅₅=16.35; conc.=1.33 mM,53.98 umol @ FW 338.30=18.26 mg. FIG. 8B: ¹⁵N₅-CEdG(A); 2 uL stockdiluted to 500; OD₂₅₅=1.207. FIG. 8C: ¹⁵N₅-CEdG(B); 1 uL stock dilutedto 500; OD₂₅₅=0.883.

FIG. 9. Proton (¹H) NMR of CEdG(A) isomer. The following parametersapply to the spectrum: transmitter freq: 399.806855 MHz; time domainsize: 21340 points; width 5208.33 Hz=13.027115 ppm=0.244064 Hz/pt;number of scans: 512; freq. of 0 ppm: 399.804642 MHz; processed size:65536 complex points; LB: 0.00; GB: 0.00.

FIG. 10. Proton (¹H)NMR of CEdG(B) isomer. The following parametersapply to the spectrum: transmitter freq: 399.806855 MHz; time domainsize: 21340 points; width 5208.33 Hz=13.027115 ppm=0.244064 Hz/pt;number of scans: 512; freq. of 0 ppm: 399.804643 MHz; processed size:65536 complex points; LB: 0.500; GB: 0.00.

FIG. 11. Carbon data: ¹³C NMR of CEdG(A). The following parameters applyto the spectrum: transmitter freq: 100.541493 MHz; time domain size:63750 points; width 24509.80 Hz=243.778000 ppm=0.384468 Hz/pt; number ofscans: 12000; freq. of 0 ppm: 100.531015 MHz; processed size: 65536complex points; LB: 0.00; GB: 0.00.

FIG. 12. Carbon data: ¹³C NMR of CEdG(B). The following parameters applyto the spectrum: transmitter freq: 100.541493 MHz; time domain size:63750 points; width 24509.80 Hz=243.778000 ppm=0.384468 Hz/pt; number ofscans: 27000; freq. of 0 ppm: 100.531015 MHz; processed size: 65536complex points; LB: 0.500; GB: 0.00.

FIG. 13. MS2 and MS3 of sodiated CEdG(A) parent ion obtained using theThermo Finnigan LTQ-FT linear ion trap mass spectrometer, showing theexpected molecular fragments for the isotopically enriched standards.

FIGS. 14A and B. Product ion scans for CEdG(A) (FIG. 14A) and¹⁵N₅-CEdG(A) (FIG. 14B) at m/z 340 and 345, respectively, showing thedaughter ions at m/z 224 and 229 monitored using a Micromass QuattroUltima Triple Quadrupole Mass Spectrometer, showing the expectedmolecular fragments for the isotopically enriched standards.

FIGS. 15A-C. Observed isotopic distributions for ¹⁵N₅-CEdG(A) (FIG. 15A)and ¹⁵N₅-CEdG(B) and the calculated isotopic distribution for C₁₃H₁₇¹⁵N₅NaO₆ (FIG. 15B) The latter was calculated using the Molecular WeightCalculator, V. 6.38 (FIG. 15C).

FIG. 16. Synthesis of oligonucleotides containing site-specificallymodified CEdGs.

FIG. 17. Consistent elevation of CEdG in obese rats, nearly 10-fold insome examples, relative to lean controls. There is consistently more (S)isomer relative to (R) in biological samples from both rodents andhumans.

FIGS. 18A-C. CEdG levels from tissue-extracted DNA in the liver (FIG.18A), pancreas (FIG. 18B) and kidney (FIG. 18C) of Zucker rats, leancontrols and Zucker rats treated with the glycation inhibitor LR-90.

FIGS. 19A-B. Measurement of urinary CEdG(R) and CEdG(S) isomers inpost-menopausal women undergoing treatment with aromatase inhibitors.

FIGS. 20A-B. CEdG(R) and CEdG(S) distribution in human solid tumors andadjacent tissue in lung, breast and kidney cancers.

DETAILED DESCRIPTION

Quantitative measurement of advanced glycation end products (AGE) isaccomplished using mass spectrometry, such as liquid chromatographyelectrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) andinternal standards designed for each targeted AGE. Such measurementsallow for precise determinations of AGE levels, including small orincremental changes in such levels.

Diabetes, metabolic disorders, cancer and other diseases may bediagnosed by measuring N²-carboxyethyl-2′-deoxyguanosine (CEdG) levelsalone or in conjunction with other AGE levels in biological samples.CEdG levels are measured using liquid chromatography electrosprayionization tandem mass spectrometry or other reliable means. The CEdGlevels from the sample are then compared to physiologically normal CEdGlevels. Methods for further determining the efficacy of therapies ortreatments applied to those disorders comprise measuring the effect theputative therapeutic have on the CEdG levels in an individual receivingit. The subject having its AGE levels and/or the efficacy of treatmentmeasured is preferably a mammal, such as a human.

Thus, one method of quantifying one or more advanced glycation endproducts in a sample, comprises obtaining a biological sample from asubject; and performing liquid chromatography electrospray ionizingtandem mass spectrometry assay on the sample using a stable isotopedilution and an internal standard to determine how much AGE is in thesample. When the AGE is N²-carboxyethyl-2′-deoxyguanosine (CEdG), theinternal standard is ¹⁵N₅-CEdG. With CEdG quantities in hand, abnormallevels may indicate metabolic disorders, cancers, or diabetes. Upondetecting the levels, efficacies of various treatments may be determinedusing AGE levels as a marker for the success of the treatment.

Metabolic diseases cover a wide range of disorders includingcarbohydrate metabolism, amino acid metabolism, organic acid metabolism,mitochondrial metabolism, porphyrin metabolism, fatty acid oxidationdisorders, purine and pyrimidine metabolism, steroid metabolism,mitochondrial metabolism, peroxisomal and lysosomal storage disorders,and glycolytic metabolic disorders, such as glyolytic cancers. Aglycolytic cancer is a cancer that is caused or influenced by abnormalsugar processing, such as with glycation. Conditions which result in theimpairment of glucose regulation such as diabetes and metabolic syndromehave been shown to significantly increase the risk for cancers of thebreast, liver, pancreas, colon, cervix and endometrium. In the case ofhyperglycemia and/or diabetes, an elevated level of CEdG, as compared tonormal physiological levels of CEdG, indicates that the subject hasdiabetes.

A sensitive LC-ESI-MS/MS method for the measurement of CEdG in urine ordouble-stranded DNA is used. Quantification is achieved by the stableisotope dilution method using synthetic ¹⁵N₅-CEdG as an internalstandard. Urinary CEdG was measured in normal and streptozoticin-induceddiabetic rats, and it was shown that adduct levels are significantlyincreased following the onset of hyperglycemia. LC-ESI-MS/MS was used todemonstrate a dose-dependent reduction in CEdG in response toadministration of LR-90, an inhibitor of AGE formation. Measurement ofCEdG from hydrolyzed and dephosphorylated double-stranded DNA wascomplicated by the fact that MG was present during the enzymatic workup.This was found to react with DNA during sample workup leading toartifactual overestimation of CEdG levels. In order to circumvent thisproblem, adventitious MG was sequestered by the addition of carbonylscavengers such as aminoguanidine (AG) and D-penicillamine (D-P) priorto workup, resulting in stable and reproducible determinations. In thecase of glycolytic cancers, such as breast cancer, a reduced level ofCEdG, as compared to normal physiological levels of CEdG, indicates thatthe subject has cancer.

Materials and Instrumentation.

¹⁵N₅-2′-deoxyguanosine was purchased from Silantes (Munich, Germany, lot#dG-N-0507-½); DL-glyceraldehyde (95%), calf thymus DNA was from Sigma(St. Louis, Mo.), and ammonium acetate (1M, pH 7 solution) from Fluka(Buchs, Switzerland). Phosphate salts were A.C.S. reagent grade fromJ.T. Baker (Phillipsburg, N.J.). High performance liquid chromatography(HPLC) grade CH₃CN was purchased from Fisher Scientific (Fair Lawn,N.J.). All water was purified to a resistivity of 18.2 MΩ using aNanopure Diamond system by Barnstead International (Dubuque, Iowa).Solid phase extractions were performed using 1 ml strata-X—C cationmixed mode cartridges (Phenomenex, Torrance Calif.). Nuclease P1 waspurchased from US Biologicals (Swampscott, Mass.). Phosphodiesterase IIfrom bovine spleen and alkaline phosphatase from bovine intestinalmucosa was purchased from Sigma-Aldrich. HPLC separations were performedusing a Hewlett-Packard Series 1100 Liquid Chromatography systemequipped with a diode-array detector. Ultraviolet spectra were collectedon an Ultrospec 3000 pro (Amersham Biosciences, Piscataway, N.J.). Massanalysis of synthetic ¹⁵N₅-CEdG was performed using a Thermo FinniganLTQ-FT linear ion trap mass spectrometer (San Jose, Calif.) in the MassSpectrometry-Proteomics Core Facility of the City of Hope.

LC-MS/MS analyses of CEdG in biological samples were carried out using aMicromass Quattro Ultima Triple Quadrupole Mass Spectrometer (Beverly,Mass.) interfaced to an Agilent 1100 Capillary HPLC system (Palo Alto,Calif.) equipped with a Synergi C₁₈ analytical column (4μ, 150×2.0 mm;Phenomenex, Torrance, Calif.). ¹H NMR spectra were recorded at 400 MHzon a VNMRS spectrometer (Varian, Inc., Palo Alto, Calif.) in theSynthesis and Biopolymer Core Facility of the City of Hope. 1D and 2DNMR data was processed using the Spinworks shareware program (version2.5.5), copyright 1999-2006 by Kirk Marat and available from theUniversity of Manitoba website.

Synthesis and Characterization of ¹⁵N₅-CEdG.

DL-Glyceraldehyde was used to generate methylgloxal (MG) in situ viaguanine catalyzed dehydration.¹⁷ DL-Glyceraldehyde (9.5 mg) was added to10 mg of ¹⁵N₅-labeled dG, 12.3 mg potassium dihydrogen phosphate, and24.0 mg disodium hydrogen phosphate in 87.7 μL H₂O. The heterogeneousreaction mixture was vortexed and placed in a heat block at 40° C.Reactions were worked up following complete dissolution of solids(˜14-17 days) yielding a yellow-red viscous solution. Products werepurified by HPLC in 10-15 μL aliquots on a 10×50 mm Waters XTerra MS C₁₈2.5μ column using a (Et)₃NH₄OAc (50 mM, pH 7)/CH₃CN gradient. The CH₃CNconcentration was raised from 0 to 4.0% in the first 5 minutes, from 4.0to 6.5% over 30 minutes; held at 6.5% for 5 minutes, then raised to 90%to wash residual material off the column. Diastereomers CEdG-A and Beluted at 24 and 29 minutes, respectively (FIG. 2).

Fractions were lyophilized to dryness prior to resuspension in 18.2 MΩH₂O. Concentrations of stock solutions were calculated by UV using amolar extinction coefficient of 12,300 @255 nm. See, for example, FIGS.8A-C. Mass analyses of ¹⁵N₅-CEdG diastereomers were conducted using aThermo-Finnigan LTQ FT ion trap mass spectrometer in the positive ionmode. A full scan MS for CEdG-A is shown in FIG. 3. The most intense ionwas observed for the sodiated peak, C₁₃H₁₇ ¹⁵N₅NaO₆ ⁺: m/z 367.18 (obs),m/z 367.09 (calc). ¹H NMR assignments for CEdG-A: ¹H NMR (400 MHz,de-DMSO, 18° C.) δ□10.60 (s, 1H, N1-H), δ 7.93 (s, 1H, C8-H), δ 6.76 (d,1H, C2-N H), δ 6.12 (dd, 1H, C1′-H), δ 5.30 (d, 1H, C3′-OH), δ 4.89(vbr, 1H, C5′-OH), δ 4.36(m, 1H, C2-NH—CH), δ 4.32 (m, 1H, C4′-H), δ3.81 (m, 1H, C3′-H), δ 3.50 (ddd, 2H, C5′-H ₂), δ 2.64 (ddd, 1H, C2′-H),δ 2.18 (ddd, 1H, C2′-H), δ 1.39 (d, 3H, C2-NH—CH—CH ₃). ¹³C NMRassignments for CEdG-A: (100.5 MHz, de-DMSO, 18° C.) δ 174.1(C2-NH—CH—COOH), δ 156.3 (C6), δ 151.5 (C2), δ 149.9 (C4), δ 136.1 (C8),δ 117.1 (C5), δ 87.6 (C3′), δ 82.9 (C1′), δ 70.8 (C4′), δ 61.7 (C5′), δ49.0 (C2-NH—CH), 6˜39.5 (C2′), δ 17.7 (C2-NH—CH—CH₃). ¹H and ¹³C NMRassignments for CEdG-B are nearly identical to the A isomer.

Synthesis of Oligonucleotides Containing Site-Specifically Modified CEdGResidues.

A synthetic scheme was devised for the quantitative preparation ofoligonucleotides containing CEdG that can be readily accommodated on anystandard DNA synthesizer using the conventional phosphoramiditetechnology. Oligos containing only pure D or L CEdG were prepared in astereochemically pure manner using D or L alanine in a reaction thatproceeds with retention of configuration. A NPE protected 2-fluoropurinephosphoramidite derivative was introduced into the polymer duringstandard oligonucleotide synthesis, and the reaction with D or L alaninewas carried out prior to any deprotection step.

Specifically, stereochemically pure (R) or (S) CEdG oligonucleotideswere synthesized by nucleophilic substitution with either (R) or (S)alanine on 2-fluorodeoxyinosine (2-Fdl) containing oligos followed bydeprotection and purification. Oligonucleotides were prepared using anAB1394 DNA synthesizer loaded with either standard or 2-F-dl-CEphosphoramidites (0.2 μM scale). For the preparation of CEdG containingoligonucleotides, F-dl-containing fully-protected oligomers still boundto the CPG support were suspended in an aqueous solution of 1M D- orL-alanine in 250 mM potassium carbonate at 50° C. for 40 hours. Completeremoval of all protecting groups was achieved by extended reaction at50° C. in concentrated ammonia for 7 days. Separation of the desiredoligonucleotide from failure sequences and other impurities was achievedby ion-pairing chromatography on a 10 mm×250 mm×Bridge Prep C18 5 μmcolumn (Waters, Milford, Mass.), using a 40 minute 9.0% to 9.5% gradientof acetonitrile vs 100 mM triethylammonium acetate (TEAA, Fluka,Milwaukee, Wis.) at a constant 45° C. All oligonucleotides werecharacterized by rechromatography under the indicated conditions andanalyzed by ESI-FT/MS on an LTQ-FT (Thermo-Finnigan, San Jose, Calif.)in the Mass Spectrometry Core of the City of Hope Cancer Center.

This new synthesis is superior to previously known syntheses for CEdGbecause it allows for the preparation of oligos containingstereochemically pure (R) or (S) CEdG in high yield. Oligos containinguniquely substituted CEdG residues are used to calibrate the biologicalmeasurement of CEdG by serving as internal standards. They are also usedin biochemical assays for examining the biological consequences ofsite-specific CEdG substitution in DNA, including, but not limited to,aspects of their repair and mutagenic potential (FIG. 16). Thissynthetic scheme may also be used to make site specific substitutionsfor other AGEs.

Stable Isotope Dilution.

Internal standards for other AGEs are usually contain stable isotopes(15N, 13C, 18O) to create a different pass from the related analyte.Different concentrations of the stable isotope substituted compounds areprepared and analyzed by MS in order to determine the response height ofthe ion current as a function of different concentrations. A calibrationplot is made of concentration vs ion current response. This is typicallya linear plot of concentrations ranging from anticipated lowestdetectable amounts to highest expected. The ion current responseincreases with concentration. To measure CEdG in a biological sample, aknown amount of stable isotope standard is “spiked” into the sample.Since the CEdG in the sample and the CEdG standard have differentmolecular weights, they can be resolved by MS. The ion current responseof the CEdG in the sample is compared to the response of the spikedistopically enriched CEdG. Since the concentration of isotopicallyenriched standard in the sample is known, comparison allows forcalculation of the amount of CEdG in the biological sample by fitting tothe calibration plot.

Stability Studies of CEdG in Acidic Solution.

A 1.25 mM solution of CEdG-A, B or dG in 100 μL of 1M AcOH (pH 2.4) wasstirred at 37° C. 10 μl aliquots were removed periodically and added to40 μL of 2M TEAA (pH 7.0). HPLC product analyses were performed using anAlltech HS HyperPrep 100 BDS C18 8μ column. A gradient of 0 to 4% CH₃CNover 5 min was followed by 6.5% CH₃CN over 30 min. TEAA (pH 7) was keptconstant at 50 mM. The ratio of free base (CEG or G) to intactnucleoside (CEdG or dG) was calculated by integration of thecorresponding HPLC peaks (see inset in FIG. 4). The CEG free base wasidentified as Peak A by ESI-MS in the negative ion mode. C₈H₈O₃N₅,observed: m/z 222.064; calculated: m/z 222.063.

Animal Studies.

All animal studies were carried out in compliance with the policiesoutlined in NIH Publication No. 85-23 “Guide for the Care and Use ofLaboratory Animals.” Male Sprague-Dawley rats were rendered diabetic byinjection of streptozoticin and maintained as previously described.¹⁸The AGE inhibitor LR-90 was administered ad libitum at concentrationsranging from 2.5-50 mg/L. Rats were housed in metabolic cages and urinewas collected over a 24 hour period with several drops of toluene toinhibit microbial growth. Urine samples were stored at −80° C. prior toLC-MS/MS analysis for CEdG. The data in FIG. 5 represent 3 replicatesfrom n different animals: non-diabetic controls, n=6; non-diabetictreated with 50 mg/L LR-90, n=5; diabetic control, n=3. For diabeticrats treated with varying doses of LR-90: 2.5 mg/L, n=4; 10 mg/L, n=5;25 mg/L, n=6; 50 mg/L, n=8.

Urine Sample Preparation.

CEdG was concentrated from urine by solid phase extraction. A 1 mlstrata-X—C cartridge was pre-conditioned by the sequential addition of 1ml MeOH/CH₃CN (1:1) followed by 2×1 ml 2% H₃PO₄. Then ¹⁵N₅-CEdG wasadded as an internal standard (final concentration 5 μg/ml), the samplewas acidified with 10 μl of 86% H₃PO₄, and finally 0.4 mL of urine wasintroduced via suction filtration. The cartridge was then washed withsequential additions of 1 ml 0.1% H₃PO₄ and 1 ml MeOH and then driedunder vacuum for 1 minute. Finally, CEdG and ¹⁵N₅-CEdG containingfractions were eluted from the cartridge with 1 mL 3% NH₄OH inMeOH:CH₃CN (2:8 v/v). The eluent was evaporated to dryness in acentrifugal concentrator and reconstituted with 200 μl 0.1% formic acidprior to LC-MS/MS injection.

Preparation of Mononucleosides from DNA.

Calf thymus or tissue-extracted DNA (100 μg) was dissolved in 80 μL ofautoclaved 18.2 MΩ H₂O containing 20 μL of sodium acetate (100 mM, pH5.5), 20 μL of 1×TBE, 1.5 μL of 50 mM ZnCl₂, and 2.37 μL of a 100 mM AGor D-P stock solution. DNA was denatured at 95° C. for 5 min on a PCRheating block and then brought to 4° C. for 5 min. After equilibrationto 45° C., 1.5 μL of 10 U/μL nuclease P1 was added. Alkaline phosphatase(4 μL of 8 U/μL), 1 U of bovine phosphodiesterase, and 14 μL of 100 mMCaCl₂ were added after 1 hour, and the hydrolysis/dephosphorylation wascontinued for another 7 hours. DNA concentrations were determined by UVspectroscopy (1 OD₂₆₀=50 μg/ml) and samples were stored at −80° C. priorto MS analyses. A 5 μL aliquot of digest was diluted to 200 μL and usedfor quantitation of 2-deoxyguanosine by HPLC integration using a BeckmanC-18 reverse phase (25 cm×4.6 mm) column (Fullerton, Calif.). Separationwas achieved isocratically using a mobile phase of 6% MeOH, 0.1% aceticacid in water.

DNA Isolation from Human Tissue.

Breast tumor and adjacent normal tissue was obtained from the frozentumor bank of the City of Hope Pathology Core. A pea-sized section (˜100mg) of tissue was minced and suspended in 1.2 mL of digestion buffer(100 mM NaCl, 10 mM Tris HCl, pH 8, 25 mM EDTA, pH 8, 0.5% SDS, 0.2mg/mL proteinase K, 10 mM D-penicillamine) and incubated at 50° C. in awater bath for 12-18 h. DNA was then extracted using an equivalentvolume of phenol/chloroform/isoamyl alcohol (25:24:1). The aqueousfraction was separated and 0.5 volumes of ammonium acetate and 2 volumesof 100% ethanol were added. The DNA was spooled, washed twice with 70%ethanol, pelleted, and resuspended in autoclaved 18.2 MΩ water. Theenzymatic hydrolysis was carried out as described above.

LC-ESI-MS/MS.

Quantification of CEdG was performed using a LC-MS/MS method.Measurement of 8-oxo-dG was performed as previously described.¹⁹ CEdGand ¹⁵N₅-CEdG (internal standard) were synthesized and purified.Measurements were performed using an Agilent 1100 Capillary LC system(Agilent Technologies, Palo Alto, Calif.) in line with a MicromassQuattro Ultima Triple Quadrupole Mass Spectrometer (Micromass, Beverly,Mass.) operating in positive-ion mode. The detector settings were asfollows: capillary voltage, 3.5 kV; cone voltage, 18 V; collision cellvoltage, 11 V; source temperature, 350° C.; desolvation temperature,150° C.; cone gas flow, 620 liter/h; and desolvation gas flow, 500liter/h. The mass transitions monitored for CEdG and ¹⁵N₅-CEdG were340.3→224.3 and 345.4→229.4 respectively. HPLC was accomplished usingisocratic conditions with a mobile phase of 15% aqueous MeOH with 0.1%formic acid on a Prodigy ODS C-18 (25 cm×2.0 mm×5 micron) column(Phenomenex, Torrance, Calif.). The flow rate was 0.2 ml/min with atotal run time of 30 min. The retention times for CEdG diastereomers Aand B using these conditions were 9.3 and 16 min, respectively. Thelower limit of quantitation for CEdG, defined as a peak height of ≥5×baseline noise, was 0.1 ng/ml in the starting solution or 0.2 pg oncolumn.

For urine analyses and calf thymus DNA digests, calibration curves wereconstructed using 0.75, 1.5, 3, 6, 12, 24, and 48 ng/mL of syntheticCEdG in urine or in blank nucleoside digestion buffer. For human breasttissues, CEdG concentrations used for calibration were 0.19, 0.38, 0.75,1.5, 3, and 6 ng/mL. Linearity of the calibration curves weredemonstrated with R-squared values of ≥0.996. Inter- and intra-dayaccuracy of the assay across the range of the standard curve wasestablished to be 96% and 94% of target concentrations, respectively.The assay was also determined to be unbiased with both inter- andintra-day precision within ±6%. Quantification of 2′-deoxyguanosine (dG)was performed by HPLC integration of DNA digests and final values wereexpressed as CEdG/10⁷dG.

Urine extracts or mononucleoside digests were spiked with 20 μL of 100ng/mL ¹⁵N₅-labeled CEdG and 10 μL of 86% phosphoric acid. Samples werethen loaded onto strata-X—C cation mixed mode columns that had beenpre-conditioned with MeOH/CH₃CN (1:4) followed by 2% phosphoric acid.After sample loading, columns were washed with 0.1% phosphoric acid,followed by MeOH. Nucleosides were eluted with 3% ammonium hydroxide inMeOH/CH₃CN (1:4) and evaporated to dryness in a centrifugalconcentrator. Samples were reconstituted with 100 μL of 0.1% formic acidand analyzed directly by LC-MS/MS. Recovery of CEdG diastereomers and¹⁵N₅-CEdG from urine and mononucleoside digests was determined to be85+/−0.9%.

Synthesis and Characterization of CEdG Isotopomers.

Isotopomers of CEdG were prepared by a modification of the method ofOchs and Severin.¹⁷ Reaction of ¹⁵N₅-dG with (dl)-glyceraldehyde inphosphate buffer afforded the desired products as a ˜1:1 mixture ofdiastereomers in ˜60% yield. Unenriched CEdG diasteromers were preparedin an analogous manner. The N² amino group of dG catalyzes thedehydration of glyceraldehyde to yield the hemiacetal of MG in situ,which then reacts to provide CEdG either directly by condensation at N²or alternatively via the rearrangement of an intermediate N¹, N² cyclicdiol. The two diastereomers of CEdG were readily resolved by HPLC andeluted at 24 and 29 minutes (FIG. 2) on a C₁₈ reverse phase column. Inspite of significant differences in chromatographic retention times,both the proton and carbon NMR spectra for CEdG-A and B were essentiallysuperimposable, with the chemical shift differential on the order of<0.1 ppm for proton and <1.0 ppm for carbon.

Mass analyses of the CEdG isotopomers were performed using a ThermoFinnigan LTQ ion trap mass spectrometer in the positive ion mode. Themost intense signal in the parent ion spectrum of the isotopicallyenriched standard corresponded to the sodium salt of ¹⁵N₅-CEdG at m/z367 [PNaH]⁺ (FIG. 3). The disodium salt [PNa₂]⁺ and the dihydro adduct[PH₂]⁺ were also observed at m/z 389 and 345, respectively. Collisioninduced dissociation of the m/z 367 parent ion gave rise primarily tothe sodiated base ion [BNaH]⁺ at m/z 251. The observed isotopicdistribution for C₁₃H₁₇ ¹⁵N₅NaO₆ was found to be in good agreement withthe calculated values.

Stability of CEdG to Acid-Catalyzed Depurination and Sidechainisomerization.

The chemical stability of CEdG was examined as an important criterionfor evaluating its suitability as a quantitative biomarker. Purifiedstereoisomers of synthetic CEdG were subjected to acidic conditions (1 MAcOH at 37° C.) and the extent of released free base and diastereomerinterconversion was monitored by HPLC as a function of time. Analogousexperiments were performed for dG and the results are presented in FIG.4. The approximate half-lives for depurination were 750 and 500 min forthe A and B isomers respectively, whereas dG was observed to be lessstable, with a half-life of 440 min under these conditions. Noracemization of the sidechain stereocenter was detected during acidichydrolysis, i.e., no interconversion of CEdG isomers A and B wasobserved.

Urinary CEdG measurement in diabetic rats. A diabetic animal model wasused to examine the relationship between glycemic status and CEdGlevels. Rats rendered diabetic by streptozoticin (STZ) treatment possesselevated MG relative to normal controls and thus appeared likely toexhibit an increased burden of CEdG adducts. The effect of AGEinhibitor, LR-90, was also examined. The results of these experimentsare shown in FIG. 5. Analyses of urine from non-diabetic control animalscollected over a 24 hr period revealed mean CEdG levels of 77 pg/ml(FIG. 5). The induction of diabetes increased the level of excreted CEdGby ˜4 fold. Administration of LR-90 to diabetic rats ad libitum at adose corresponding to 2.5 mg/L resulted in a 2.3 fold decrease in CEdGtiter. Increasing concentrations of LR-90 led to a dose dependentreduction in CEdG, and at 25 mg/L the adduct level in urine wascomparable to that of non-diabetic animals. In contrast, administrationof LR-90 at doses up to 50 mg/L in normal controls had no significanteffect on CEdG levels. 8-oxo-dG was also measured as an indicator ofoxidative stress in normal and diabetic rats; however, excreted 8-oxo-dGin diabetic animals was not statistically different (P>0.05) fromcontrols.

CEdG in Organs of Zucker Fatty Rats.

The Zucker rat is a morbidly obese, hyperinsulinemic model for Type 2diabetes resulting from homozygous knockout of the leptin receptor. Inorder to determine whether elevated circulating glucose in the Zuckerrat correlates with increased tissue DNA glycation, CEdG levels fromtissue-extracted DNA were measured in selected organs and compared tolean controls and to Zucker rats treated with the glycation inhibitorLR-90. Data for liver, pancreas and kidney are shown in FIGS. 18A-C.Relative to lean rats, CEdG levels were found to be elevated only inkidneys. In lean animals, CEdG was below the level of detection in 9/9animals, whereas it was elevated in 5/9 Zucker rats. All three organs ofZucker rats had a net lowering of CEdG levels following treatment withLR-90. These data show that CEdG determination can be used to monitortissue glycation levels in response to chemotherapy.

CEdG in Calf Thymus DNA.

Commercial grade calf thymus DNA was used as a model substrate fordeveloping a protocol for CEdG quantitation in double-stranded DNA. DNAwas hydrolyzed and dephosphorylated by sequential addition of nucleaseP1, alkaline phosphatase and phosphodiesterase. Then, mononucleosideswere concentrated by solid phase extraction prior to LC-MS/MS analyses.The results of these experiments are shown in FIG. 6. Initialdeterminations yielded values of CEdG in the range of 60-66 CEdG/10⁶ dG.These surprisingly high levels showed that some CEdG may have beenformed artifactually during the hydrolysis and dephosphorylation.Additional CEdG may have been formed due to the release of MG from theprotein reagents used in the workup during prolonged incubation.Proteins can bind MG reversibly, and up to 90% of cellular MG may besequestered in this manner. In order to prevent additional reactions ofadventitiously generated MG with DNA, carbonyl scavenging agents AG orD-P were added prior to DNA digestion and dephosphorylation. Thesereagents sequester MG and other alpha-oxoaldehydes by forming stablecyclic aminotriazine and thiazolidine derivatives respectively.Concentrations of AG from 0.5 to 50 mM were added prior to workup, andCEdG levels were measured in order to determine the optimalconcentration required to achieve stable, reproducible levels. Theaddition of 10 mM AG prior to sample processing resulted in a modest butsignificant drop in adduct levels (45-50 CEdG/10⁶ guanines) in calfthymus DNA, suggesting that ˜15 CEdG/10⁶ guanines were formed as adirect result of the hydrolysis and dephosphorylation protocol.

Since the extraction of DNA from biological samples requires extendedreaction with proteinase K (up to 24 h), it was investigated whetherthis treatment could also contribute to artifactual CEdG formation.Accordingly, calf thymus DNA was subjected to mock proteolysis prior tohydrolysis and workup in the absence of carbonyl scavenger. FIG. 6reveals an increase in adduct levels significantly higher than thoseobserved following hydrolysis alone, with values ranging from 80-100CEdG/10⁶ guanines. The addition of 10 mM AG in two aliquots prior to themock lysis treatment and hydrolysis/dephosphorylation steps resulted ina drop in measured CEdG levels comparable to that observed previouslyfor calf thymus DNA subjected only to the hydrolysis/dephosphorylationin the presence of AG. No apparent stereoisomer bias was detected in anyof these samples, i.e., the ratio of CEdGA: CEdGB was not significantlydifferent from 1:1.

Measurement of Urinary CEdG in Post-Menopausal Women UndergoingTreatment with Aromatase Inhibitors.

One noted side-effect of treatment with aromatase inhibitors (AI) incancer therapy is an impairment of cognitive function, which may belinked to enhanced glycation in the brain. Enhanced brain glycation is acontributing factor in the pathology of Alzheimer's disease. In order toexamine whether treatment with aromatase inhibitors can affect glycationstatus, urine from 32 patients was collected just prior to and 6 monthsfollowing administration of AI, and levels of CEdG were measured inurine. Data for the (R) and (S) isomers of CEdG are shown in panels Aand B, respectively, of FIGS. 19A-B. In the case of the (R) isomer,12/32 patients show significantly higher levels after AI treatment, atrend also observed for 14/32 patients when levels of the (S) isomer areconsidered. Some of these post-treatment levels are very high, muchhigher than any observed pre-treatment levels. There is also goodconsistency between the two independent biomarkers. For example, inpatients 3, 6, 9, 12, 13, 17, 18, 20, 23, 24, 29 and 30, bothstereoisomers are elevated post-AI treatment. If these changes arecorrelated with decreased mental acuity over time, CEdG measurement canalso be used to identify patients at risk for cognitive impairment.Additionally, one or more CEdG inhibitors, such as LR-90, may beadministered to a subject undergoing chemotherapy in order to prevent orreduce the cognitive impairment that may accompany chemotherapy.

CEdG Measurement in Human Solid Tumors Vs Adjacent Tissue.

Frozen tumor specimens and adjacent tissue were obtained from the Cityof Hope Tumor Bank. DNA was extracted as described and analyzed forCEdG. Results are shown in FIGS. 20A-B for (R) and (S) CEdG in lung,breast and kidney cancers. In lung cancers CEdG was observed at lowerlevels in tumor relative to adjacent tissue in the majority of samples.This same phenomenon was observed for the single breast cancer sampleanalyzed. These trends are followed for both isomers. In the case ofkidney cancers, the situation is more complex, with samples 3 and 6showing the opposite trend of higher CEdG in tumor relative to adjacenttissue. In sample 6, the levels of (R) and (S) isomers were 13 and 18fold higher respectively in tumor relative to adjacent tissue. Othersamples, such as 1, 4 and 5, follow the trend observed in the lung andbreast samples.

These variations in CEdG between tumor and adjacent tissue represent thecorresponding levels of glycolytic stress. In order to avoid thepro-apoptotic effects of methylglyoxal produced as a result of enhancedglycolysis, solid tumors must restrict its accumulation. Tumors withlower levels of CEdG relative to adjacent tissue, can successfullyminimize their glycolytic stress in spite of maintaining elevatedglycolysis. This is likely due to overexpression of the methylglyoxalscavenging enzymes glyoxalase 1 and aldose reductase in tumors, as wellas enhanced removal of CEdG from DNA by repair enzymes. Tumors withelevated levels of CEdG relative to adjacent tissue are predicted to begenetically unstable, and more sensitive to chemotherapy as a result ofthe cytotoxic accumulation of methylglyoxal. Thus, another embodiment isa method of predicting which tumors of a cancer patient are moresusceptible to chemotherapy by testing CEdG levels in tumor samples. Ifthe CEdG levels are high, then the tumor is more likely to be receptiveto chemotherapy treatment. Measurement of CEdG can also be used toidentify which cancers which can benefit from targeting glyoxalase 1and/or aldose reductase, in order to restore their sensitivity tochemotherapy. CEdG measurement can provide a direct means foridentifying tumors most likely to benefit from these approaches.

Quantitation of CEdG in a Human Breast Tumor and Adjacent Normal Tissue.

Many cancer cells in the hyopoxic tumor microenvironment primarilyutilize glycolysis to meet their energetic demands. This glycolyticphenotype (Warburg effect) is characterized by constitutive cell surfaceexpression of glucose transporter proteins such as GLUT-1, and forms thebasis for the diagnostic use of ¹⁸FDG-PET in the imaging of breast andother cancers.^(26,27) Enhanced glyocolytic flux suggests that breasttumors might exhibit abnormal levels of AGEs including CEdG. Accordinglythe levels of CEdG diastereomers were measured in DNA extracted from aclinical breast tumor specimen as well as adjacent normal tissue. Thedata in Table 1 reveal some significant (P<0.05) differences in thelevels of CEdG between tumor and normal tissue. Both stereoisomers wereobserved at ˜3-fold higher levels in normal relative to tumor tissue(CEdG-A, P=0.02; CEdG-B, P=0.003). In the column under CEdG/107dG, “a”indicates P=0.08 versus CEdG-B in normal issue; “b” indicates P=0.02versus CEdG-A in adjacent normal tissue; “c” indicates P=0.003 versusCEdG-B in adjacent tumor tissue; and “d” indicates P=0.03 versus CEdG-Ain tumor tissue.

TABLE 1 CEdG isomers from a human breast tumor and adjacent normaltissue. CEdG (fmol) dG (fmol) CEdG/10⁷ dG CEdG-A Normal 234 ± 24.9 1.91× 10⁸ 12.3^(a) ± 1.3  Tumor 247 ± 11.6 6.48 × 10⁸ 3.9^(b) ± 0.2 CEdG-BNormal 151 ± 4.98 1.91 × 10⁸ 7.9^(c) ± 0.3 Tumor 173 ± 6.64 6.48 × 10⁸2.7^(d) ± 0.1 ^(a)P = 0.08 versus CEdG-B in normal tissue. ^(b)P = 0.02versus CEdG-A in adjacent normal tissue. ^(c)P = 0.003 versus CEdG-B inadjacent tumor tissue. ^(d)P = 0.03 versus CEdG-A in tumor tissue.

Within normal tissue, the levels of CEdG-A and B were not significantlydifferent (P=0.08), while in tumor there was a small bias favoringCEdG-A (P=0.03). Levels of CEdG in DNA extracted from either breasttumor or adjacent tissue in the absence of carbonyl scavenger were˜1.5-2.0 fold higher; however, artifactual formation was inhibited bythe addition of 10 mM D-penicillamine in two aliquots during both thecell lysis/DNA isolation and hydrolysis/dephosphorylation steps.¹⁵N-enriched isotopomers of CEdG differing from the unlabelled adductsby 5 amu were synthesized, which provided sufficient mass resolution foraccurate and reproducible quantitation using the stable isotope dilutionmethod.

The ability to simultaneously resolve and quantitate both diastereomersof CEdG provides two independent parameters for assessing DNA glycationlevels within a single sample. The biological significance of the CEdGdiastereomer ratio in vivo may reflect stereochemical biases in adductrepair or polymerase bypass. Of course, examination of the CEdGstereoisomer distribution in vivo by LC-ESI-MS/MS would only bemeaningful if the rate of stereochemical interconversion was negligible.Regarding overall adduct stability, loss of the CEG base from eitherstereoisomer during workup would result in the generation of abasicsites leading to an underestimation of true nucleoside adduct levels,which was of particular concern since CEdG undergoes depurination morereadily than dG at elevated temperatures. The extent of depurination andracemization was quantified by monitoring free base formation and isomerinterconversion under acidic conditions at 37° C. rather than atnon-physiological temperatures. FIG. 4 shows that the CEdG diastereomerspossess similar stability, and are slightly more resistant todepurination under acidic conditions than dG. This fact, together withthe prohibitive barrier to stereochemical interconversion, indicatesthat determination of CEdG diastereomer ratios may be plausibly used inquantitative biomarker studies. Various quantifications of CEdG arefound in FIGS. 9-15.

One important confounding factor in the quantitation of adductsresulting from oxidative or oxoaldehyde DNA modification is artifactualproduct formation during sample isolation and workup. The problemssurrounding the measurement of 8-oxo-dG using GC-MS and/or mildlyoxidizing workup conditions have been detailed previously.³⁶⁻³⁸ In thecase of CEdG adducts, the presence of MG during the workup couldcomplicate the accurate determination of endogenous levels. The effectsof carbonyl scavenger addition prior to the enzymatic digestions wereexamined due to the high background levels of CEdG detected in reagentgrade calf thymus DNA. Scavengers such as AG and D-P react rapidly withMG and other oxoaldehydes to yield aminotriazines and thiazolidinesrespectively (FIG. 7) which are relatively unreactive electrophiles.D-penicillamine reacts with MG 60 times faster than AG, and thus may bemore advantageous for CEdG determinations requiring DNA isolation fromcomplex tissue matrices.

MG bound reversibly to proteins was predominantly responsible for theformation of DNA glycation artifacts observed during the isolation andworkup of dsDNA. Extraction and workup procedures which expose DNA forextended periods to cell lysates and partially purified enzyme reagentsincrease the probability for the ex vivo formation of CEdG,necessitating the need for carbonyl scavengers. MG-BSA conjugatesprepared by incubating MG with BSA can be used as reagents to induce DNAdamage in cultured mammalian cells. The data in FIG. 6 suggest that theaddition of AG or D-P can largely eliminate artifactual CEdG formation.Minimizing exposure to proteins by shortening the enzymatic lysis andhydrolysis/dephosphorylation steps may also reduce the requirement forcarbonyl scavengers.

A diverse array of tumor and corresponding control tissues are examinedin order to determine whether the trends noted in the breast cancerspecimen are a general feature of tumors which display elevated levelsof glycolysis. The finding of significantly lower CEdG in breast tumorsrelative to adjacent normal tissue can potentially be explained by theobservation that glycolytic cancers possess lower levels of MG as aresult of overexpression of the glyoxalase system. This highlyevolutionarily conserved system consists of two non-homologous zincmetalloenzymes Glo1 and Glo2, which act sequentially to convert MG intolactate using reduced glutathione (GSH) as a catalytic cofactor.

Glo1/2 are overexpressed around 3-5× in many breast cancers relative tonormal mammary tissue, and enhanced expression of either one or bothenzymes has also been observed in prostate, kidney, lung, colon,stomach, brain and ovarian cancers.⁴²⁻⁴³ This is a metabolic adaptationto counter the pro-apoptotic effect of MG accumulation in glycolytictumors, which make Glo1 and Glo2 inhibitors attractive candidates forcancer therapeutics. Accordingly, another application of the presentquantitative LC-MS/MS method is for monitoring the efficacy ofglyoxalase inhibitors, which would induce a dose dependent increase inCEdG levels.

In sum, the new quantitative LC-MS/MS method for the measurement of CEdGimproves upon (with purity and volume) and complements methods currentlyavailable for detecting protein AGEs, and allows for a morecomprehensive evaluation of the role of nucleotide glycation in a widerange of human metabolic diseases, including diseases in which CEdGlevels affect the disease.

The foregoing merely illustrates various embodiments. As such, thespecific modifications discussed above are not to be construed aslimitations on the scope of the disclosed products and methods.Equivalent embodiments are included within the contemplated scope. Allreferences cited herein are incorporated by reference as if fully setforth herein.

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The invention claimed is:
 1. A method of treating diabetes in a subjectcomprising: (i) quantifying a N²-carboxyethyl-2′-deoxyguanosine (CEdG)level in a urine sample from the subject comprising: (a) performing aliquid chromatography electrospray ionizing tandem mass spectrometry(LC-ESI-MS/MS) assay on the urine sample using a stable isotope dilutioncomprising using an internal ¹⁵N₅-carboxyethyl-2′-deoxyguanosine(¹⁵N₅-CEdG) standard comprising stereochemically pure (R) andstereochemically pure (S)¹⁵N₅-CEdG; and (b) measuring the CEdG level inthe urine sample; (ii) determining the subject has diabetes when theCEdG level in the urine sample is elevated as compared to a normalphysiological CEdG level; and (iii) administering a treatment fordiabetes to the subject determined to have diabetes.
 2. The method ofclaim 1, further comprising preventing artifactual CEdG formation byadding aminoguanidine and/or D-penicillamine to the sample prior toquantifying the CEdG level in the sample.
 3. The method of claim 1,wherein quantifying the level of CEdG comprises quantifying the level ofCEdG (S) and CEdG (R).
 4. The method of claim 1, wherein the internal¹⁵N₅-CEdG standard comprises oligonucleotides containingstereochemically pure ¹⁵N₅-CEdG (R) and oligonucleotides containingstereochemically pure ¹⁵N₅-CEdG (S).
 5. A method of treating diabetes ina subject comprising: (i) quantifying aN²-carboxyethyl-2′-deoxyguanosine (CEdG) level in a urine sample fromthe subject comprising using an internal¹⁵N₅-carboxyethyl-2′-deoxyguanosine (¹⁵N₅-CEdG) standard comprisingstereochemically pure (R) and stereochemically pure (S) ¹⁵N₅-CEdG; (ii)determining the subject has diabetes when the CEdG level in the urinesample is elevated as compared to a normal physiological CEdG level; and(iii) administering a treatment for diabetes to the subject determinedto have diabetes.
 6. The method of claim 5, wherein quantifying thelevel of CEdG comprises quantifying the level of CEdG (S) and CEdG (R).7. The method of claim 5, further comprising preventing artifactual CEdGformation by adding aminoguanidine and/or D-penicillamine to the sampleprior to quantifying the CEdG level in the sample.
 8. The method ofclaim 5, wherein the internal ¹⁵N₅-CEdG standard com prisesoligonucleotides containing stereochemically pure ¹⁵N₅-CEdG (R) andoligonucleotides containing stereochemically pure ¹⁵N₅-CEdG (S).
 9. Themethod of claim 8, further comprising preventing artifactual CEdGformation by adding aminoguanidine and/or D-penicillamine to the sampleprior to quantifying the CEdG level in the sample.
 10. The method ofclaim 9, wherein quantifying a CEdG level in a urine sample from thesubject comprises: (a) performing a liquid chromatography electrosprayionizing tandem mass spectrometry (LC-ESI-MS/MS) assay on the urinesample using a stable isotope dilution using the internal ¹⁵N₅-CEdGstandard; and (b) measuring the CEdG level in the urine sample.